Learn R Programming
RnBeads (version 1.4.0)

data.frame2GRanges: data.frame2GRanges

Description

Converts a data.frame that defines genomic regions to object of type GRanges.

Usage

data.frame2GRanges(dframe, ids = rownames(dframe), chrom.column = "chromosome", start.column = "start", end.column = "end", strand.column = NULL, assembly = "hg19", sort.result = TRUE)

Arguments

dframe
Table defining genomic regions.
ids
Region names (identifiers) as a character vector, or NULL if no names are present.
chrom.column
Column name or index that lists the chromosome names.
start.column
Column name or index that lists the start positions of the regions.
end.column
Column name or index that lists the end positions of the regions.
strand.column
Column name or index that lists the strands on which the regions are located. Set this to NULL if this region set is not strand-specific.
assembly
Genome assembly of interest. See rnb.get.assemblies for the list of supported genomes.
sort.result
Should the resulting table be sorted

Value

GRanges object encapsulating all well defined regions on supported chromosomes, contained in dframe. Columns other that the ones listed as parameters in this function are included as metadata.